A new method of growing a semi-insulating GaN layer for high electron mobility transistor (HEMT) structure by eliminating a degenerate layer located at the GaN/sapphire interface is proposed. In the process, during the temperature ramp-up after the growth of a low temperature GaN buffer layer, trimethylgallium (TMGa) was flowed into the reactor together with ammonia, leading to the growth of an additional GaN layer of high carbon concentration. We confirmed that the introduction of TMGa induced high carbon concentration in the degenerate layer. The incorporated carbon formed deep acceptors, CN, compensating donors such as ON, resulting in the elimination of the degenerate layer. A HEMT device made on the sample grown by the new growth process shows a good pinch-off characteristic and high off-state breakdown voltage over 800 V at a gate voltage of −4 V, indicating the new scheme is effective to grow a high quality semi-insulating GaN layer.